Today I just wanted to add the Windows Azure Certificate to my Eclipse IDE (WindowsAzure4e).
I misstyped the cert password and get this error:

javax.crypto.BadPaddingException: Given final block not properly padded

But then I didn’t get the dialog again to enter the right password.

To get this problem solved you need to delete the imported windows azure certs settings in eclipse.

To do so just delete this folder:

ECLIPSE_WORKSPACE/.metadata/.plugins/org.soyatec.windows.azure.core

Then you can repeat adding the certificate.

Maybe it also helps to delete the certificate completely from your system. To do so start the windows cert manger:

Start -> Search -> certmgr.msc -> Enter

Search for the installed cert in the different cert folders and delete it.